Covalent organic frameworks (COFs) have been increasingly used in capillary electrochromatography due to their excellent characteristics. In this work, hydrazine-linked TFPB-DHzDS (TFPB: 1,3,5-tris(4-formylphenyl)benzene; DHzDS: 2,5-bis(3-(ethylthio)propoxy)terephthalohydrazide) was first synthesized by a simpler and easier method at room temperature and introduced into capillary electrochromatography as coating material. The TFPB-DHzDS coated capillaries were prepared by an in-situ growth process at room temperature. After optimizing the coating concentration and experimental conditions of capillary electrochromatography, baseline separation of two groups of polycyclic aromatic hydrocarbons was achieved based on the TFPB-DHzDS coated capillary. And the established method was used successfully to determine PAHs in natural water and soil samples. The spiked recoveries of polycyclic aromatic hydrocarbons in these samples ranged from 90.01% to 111.0%, indicating that the method is reliable and could detect polycyclic aromatic hydrocarbons in natural samples. Finally, molecular simulation was applied to study and visualize the interaction between the analytes and coating COF materials to investigate the molecular level separation mechanism further.